TY - JOUR
T1 - MARVEL-minimising the emergence and dissemination of HIV-1 drug resistance in Portuguese-speaking African Countries (PALOP)
T2 - low-cost portable NGS platform for HIV-1 surveillance in Africa
AU - Sebastião, Cruz S.
AU - Pingarilho, Marta
AU - Bathy, Jamila
AU - Bonfim, Elizângela
AU - Toancha, Katia
AU - Miranda, Mafalda N. S.
AU - Martins, M. Rosário O.
AU - Gomes, Perpétua
AU - Lázaro, Lazismino
AU - Pina-Araújo, Isabel
AU - Nhampossa, Tacilta
AU - Leal, Silvania
AU - Abecasis, Ana B.
AU - Pimentel, Victor
N1 - Funding Information:
Foundation for Science and Technology (FCT) funded the MARVEL project (PTDC/SAU-PUB/4018/2021), GHTM (GHTM-UID/04413/2020), LA-REAL-LA/P/0117/2020 supporting the costs related to project implementation in Cape Verde, Mozambique and Sao Tome & Principe. Calouste Gulbenkian Foundation (FCG), under the ENVOLVE Ci\u00EAncia PALOP program, funded the HITOLA project (Number 250466), which is supporting the costs related to the project implementation in Angola. The funders have no role in the conceptualization, design, data collection, analysis, decision to publish, or preparation of the manuscript.
Publisher Copyright:
© The Author(s) 2024.
PY - 2024/12
Y1 - 2024/12
N2 - Background: HIV-1 infections remain a global public health concern. Scaled-up antiretroviral treatment (ART) is crucial for reducing morbidity and mortality related to HIV/AIDS. The emergence of drug-resistance mutations (DRMs) compromises viral suppression and contributes to the continued HIV-1 transmission. Several reports indicate a recent increase in acquired (ADR) and transmitted (TDR) drug resistance in Africa, probably linked to the lack of implementation of HIV drug resistance (HIVDR) testing and suboptimal treatment adherence. Herein, we will develop a low-cost protocol using third-generation sequencing (Oxford Nanopore Technology) for HIV-1 surveillance in Portuguese-speaking African Countries - PALOP [Angola (AO), Cape Verde (CV), Mozambique (MZ), and Sao Tome & Principe (STP)]. Methods: This is a multicentric cross-sectional study that includes around 600 adult patients newly diagnosed with HIV-1 in the PALOP. An epidemiological questionnaire previously validated by our research team will be used to collect sociodemographic and clinical data. Also, whole blood samples will be collected and the plasma samples will be subjected to drug resistance testing using an in-house low-cost NGS protocol. Data analysis will involve bioinformatics, biostatistics and machine learning techniques to generate accurate and up-to-date information about HIV-1 genetic diversity, ADR and TDR. Discussion: The implementation of this low-cost NGS platform for HIV-1 surveillance in the PALOP will allow: (i) to increase DRM surveillance capacity in resource-limited settings; (ii) to understand the pattern and determinants of dissemination of resistant HIV-1 strains; and (iii) to promote the development of technical and scientific skills of African researchers for genomic surveillance of viral pathogens and bioinformatics analysis. These objectives will contribute to reinforcing the capacity to combat HIV infection in Africa by optimizing the selection of ART regimens, improving viral suppression, and reducing ADR or TDR prevalence in PALOPs, with relevant implications for public health.
AB - Background: HIV-1 infections remain a global public health concern. Scaled-up antiretroviral treatment (ART) is crucial for reducing morbidity and mortality related to HIV/AIDS. The emergence of drug-resistance mutations (DRMs) compromises viral suppression and contributes to the continued HIV-1 transmission. Several reports indicate a recent increase in acquired (ADR) and transmitted (TDR) drug resistance in Africa, probably linked to the lack of implementation of HIV drug resistance (HIVDR) testing and suboptimal treatment adherence. Herein, we will develop a low-cost protocol using third-generation sequencing (Oxford Nanopore Technology) for HIV-1 surveillance in Portuguese-speaking African Countries - PALOP [Angola (AO), Cape Verde (CV), Mozambique (MZ), and Sao Tome & Principe (STP)]. Methods: This is a multicentric cross-sectional study that includes around 600 adult patients newly diagnosed with HIV-1 in the PALOP. An epidemiological questionnaire previously validated by our research team will be used to collect sociodemographic and clinical data. Also, whole blood samples will be collected and the plasma samples will be subjected to drug resistance testing using an in-house low-cost NGS protocol. Data analysis will involve bioinformatics, biostatistics and machine learning techniques to generate accurate and up-to-date information about HIV-1 genetic diversity, ADR and TDR. Discussion: The implementation of this low-cost NGS platform for HIV-1 surveillance in the PALOP will allow: (i) to increase DRM surveillance capacity in resource-limited settings; (ii) to understand the pattern and determinants of dissemination of resistant HIV-1 strains; and (iii) to promote the development of technical and scientific skills of African researchers for genomic surveillance of viral pathogens and bioinformatics analysis. These objectives will contribute to reinforcing the capacity to combat HIV infection in Africa by optimizing the selection of ART regimens, improving viral suppression, and reducing ADR or TDR prevalence in PALOPs, with relevant implications for public health.
KW - Africa
KW - Drug resistance
KW - HIV-1
KW - Machine learning
KW - PALOP
UR - http://www.scopus.com/inward/record.url?scp=85202873094&partnerID=8YFLogxK
U2 - 10.1186/s12879-024-09803-1
DO - 10.1186/s12879-024-09803-1
M3 - Article
C2 - 39210296
AN - SCOPUS:85202873094
SN - 2374-4235
VL - 24
JO - BMC Infectious Diseases
JF - BMC Infectious Diseases
IS - 1
M1 - 884
ER -